Starting phenix.real_space_refine on Wed Jun 3 10:11:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xko_66973/06_2026/9xko_66973.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1849 2.51 5 N 463 2.21 5 O 765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3083 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2854 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 21, 'TRANS': 346} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Classifications: {'water': 207} Link IDs: {None: 206} Time building chain proxies: 0.85, per 1000 atoms: 0.28 Number of scatterers: 3083 At special positions: 0 Unit cell: (51.2691, 64.989, 77.9868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 765 8.00 N 463 7.00 C 1849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 93.8 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 678 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 5 sheets defined 53.5% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 68 through 78 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.906A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.490A pdb=" N ASP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.902A pdb=" N GLU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.544A pdb=" N SER A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.434A pdb=" N LEU A 33 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 35 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 85 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 34 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 87 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP A 36 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ALA A 89 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY A 286 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 136 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 288 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.434A pdb=" N LEU A 33 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 35 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 85 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 34 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE A 87 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP A 36 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ALA A 89 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 173 removed outlier: 8.406A pdb=" N SER A 171 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR A 251 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU A 173 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N ASN A 253 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA A 249 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 198 removed outlier: 3.835A pdb=" N LYS A 196 " --> pdb=" O ASP A 203 " (cutoff:3.500A) 142 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 916 1.34 - 1.46: 497 1.46 - 1.57: 1520 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2945 Sorted by residual: bond pdb=" C1 GLC B 1 " pdb=" O5 GLC B 1 " ideal model delta sigma weight residual 1.402 1.501 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 GLC B 2 " pdb=" O5 GLC B 2 " ideal model delta sigma weight residual 1.402 1.501 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C5 GLC B 2 " pdb=" O5 GLC B 2 " ideal model delta sigma weight residual 1.415 1.472 -0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" C5 GLC B 1 " pdb=" O5 GLC B 1 " ideal model delta sigma weight residual 1.415 1.471 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C2 GLC B 2 " pdb=" C3 GLC B 2 " ideal model delta sigma weight residual 1.528 1.481 0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 2940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 3776 0.93 - 1.86: 155 1.86 - 2.79: 33 2.79 - 3.73: 27 3.73 - 4.66: 8 Bond angle restraints: 3999 Sorted by residual: angle pdb=" CB GLU A 70 " pdb=" CG GLU A 70 " pdb=" CD GLU A 70 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.70e+00 3.46e-01 4.55e+00 angle pdb=" CG LYS A 128 " pdb=" CD LYS A 128 " pdb=" CE LYS A 128 " ideal model delta sigma weight residual 111.30 115.59 -4.29 2.30e+00 1.89e-01 3.47e+00 angle pdb=" CA GLU A 70 " pdb=" CB GLU A 70 " pdb=" CG GLU A 70 " ideal model delta sigma weight residual 114.10 117.30 -3.20 2.00e+00 2.50e-01 2.56e+00 angle pdb=" C1 GLC B 1 " pdb=" O5 GLC B 1 " pdb=" C5 GLC B 1 " ideal model delta sigma weight residual 116.10 111.48 4.62 3.00e+00 1.11e-01 2.38e+00 angle pdb=" C ILE A 252 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " ideal model delta sigma weight residual 121.80 119.25 2.55 1.71e+00 3.42e-01 2.22e+00 ... (remaining 3994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1565 16.87 - 33.73: 161 33.73 - 50.60: 39 50.60 - 67.46: 15 67.46 - 84.33: 4 Dihedral angle restraints: 1784 sinusoidal: 724 harmonic: 1060 Sorted by residual: dihedral pdb=" CA ASP A 206 " pdb=" CB ASP A 206 " pdb=" CG ASP A 206 " pdb=" OD1 ASP A 206 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU A 240 " pdb=" CG GLU A 240 " pdb=" CD GLU A 240 " pdb=" OE1 GLU A 240 " ideal model delta sinusoidal sigma weight residual 0.00 84.33 -84.33 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " pdb=" CG1 ILE A 28 " pdb=" CD1 ILE A 28 " ideal model delta sinusoidal sigma weight residual 60.00 116.82 -56.82 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 1781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 240 0.025 - 0.050: 123 0.050 - 0.075: 37 0.075 - 0.100: 23 0.100 - 0.126: 17 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA ASN A 308 " pdb=" N ASN A 308 " pdb=" C ASN A 308 " pdb=" CB ASN A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 252 " pdb=" N ILE A 252 " pdb=" C ILE A 252 " pdb=" CB ILE A 252 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE A 142 " pdb=" N ILE A 142 " pdb=" C ILE A 142 " pdb=" CB ILE A 142 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 437 not shown) Planarity restraints: 515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 370 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ARG A 370 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG A 370 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 371 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 371 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR A 371 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 371 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 367 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C TYR A 367 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR A 367 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 368 " 0.009 2.00e-02 2.50e+03 ... (remaining 512 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 2061 3.05 - 3.51: 3268 3.51 - 3.97: 6054 3.97 - 4.44: 7185 4.44 - 4.90: 10154 Nonbonded interactions: 28722 Sorted by model distance: nonbonded pdb=" N GLU A 70 " pdb=" OE1 GLU A 70 " model vdw 2.585 3.120 nonbonded pdb=" N THR A 312 " pdb=" O THR A 312 " model vdw 2.625 2.496 nonbonded pdb=" N THR A 251 " pdb=" O THR A 251 " model vdw 2.637 2.496 nonbonded pdb=" CG LYS A 215 " pdb=" NZ LYS A 215 " model vdw 2.643 2.816 nonbonded pdb=" N TRP A 88 " pdb=" O TRP A 88 " model vdw 2.649 2.496 ... (remaining 28717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.200 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 2946 Z= 0.216 Angle : 0.548 4.658 4002 Z= 0.273 Chirality : 0.041 0.126 440 Planarity : 0.004 0.026 515 Dihedral : 15.561 84.326 1106 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.34 % Allowed : 15.88 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.44), residues: 366 helix: 0.27 (0.38), residues: 182 sheet: 0.57 (1.06), residues: 23 loop : 1.13 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.014 0.002 PHE A 73 TRP 0.009 0.001 TRP A 184 HIS 0.004 0.002 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 ( 2945) covalent geometry : angle 0.54653 / 0.27 ( 3999) hydrogen bonds : bond 0.13471 / 8.80 ( 138) hydrogen bonds : angle 7.08613 / 5.21 ( 411) link_ALPHA1-4 : bond 0.00225 / 0.12 ( 1) link_ALPHA1-4 : angle 1.40074 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.129 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 300 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6764 (mp0) REVERT: A 317 GLU cc_start: 0.7956 (tt0) cc_final: 0.7430 (tp30) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.7605 time to fit residues: 25.6296 Evaluate side-chains 32 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108449 restraints weight = 3107.196| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.06 r_work: 0.3111 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2946 Z= 0.181 Angle : 0.574 4.838 4002 Z= 0.304 Chirality : 0.044 0.126 440 Planarity : 0.004 0.038 515 Dihedral : 4.913 50.159 427 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.70 % Allowed : 13.51 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.43), residues: 366 helix: 0.61 (0.36), residues: 183 sheet: 0.36 (1.05), residues: 24 loop : 1.11 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 342 TYR 0.016 0.002 TYR A 309 PHE 0.021 0.003 PHE A 111 TRP 0.011 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 2945) covalent geometry : angle 0.57134 / 0.30 ( 3999) hydrogen bonds : bond 0.05725 / 3.88 ( 138) hydrogen bonds : angle 5.23438 / 3.80 ( 411) link_ALPHA1-4 : bond 0.00303 / 0.16 ( 1) link_ALPHA1-4 : angle 2.00343 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.126 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 300 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6773 (mp0) REVERT: A 304 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7885 (tp30) outliers start: 8 outliers final: 4 residues processed: 33 average time/residue: 0.6822 time to fit residues: 23.1219 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110922 restraints weight = 3122.130| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.05 r_work: 0.3143 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2946 Z= 0.121 Angle : 0.490 4.672 4002 Z= 0.258 Chirality : 0.041 0.122 440 Planarity : 0.004 0.040 515 Dihedral : 4.655 51.076 427 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.03 % Allowed : 14.53 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.43), residues: 366 helix: 0.97 (0.36), residues: 180 sheet: 0.35 (1.06), residues: 24 loop : 1.14 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.013 0.002 PHE A 118 TRP 0.011 0.001 TRP A 184 HIS 0.003 0.002 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 2945) covalent geometry : angle 0.48757 / 0.26 ( 3999) hydrogen bonds : bond 0.04744 / 3.23 ( 138) hydrogen bonds : angle 4.93056 / 3.57 ( 411) link_ALPHA1-4 : bond 0.00171 / 0.09 ( 1) link_ALPHA1-4 : angle 1.77619 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.119 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7290 (tt0) REVERT: A 265 LYS cc_start: 0.7327 (mtpt) cc_final: 0.6841 (mtmt) REVERT: A 300 GLU cc_start: 0.7647 (mm-30) cc_final: 0.6738 (mp0) REVERT: A 304 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7766 (tp30) outliers start: 6 outliers final: 2 residues processed: 34 average time/residue: 0.7136 time to fit residues: 24.8225 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 354 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110446 restraints weight = 3067.851| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.04 r_work: 0.3138 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2946 Z= 0.131 Angle : 0.498 4.720 4002 Z= 0.263 Chirality : 0.041 0.122 440 Planarity : 0.004 0.040 515 Dihedral : 4.681 51.103 427 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.03 % Allowed : 14.86 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.42), residues: 366 helix: 1.03 (0.36), residues: 180 sheet: 0.33 (1.06), residues: 24 loop : 1.12 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.014 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 2945) covalent geometry : angle 0.49626 / 0.26 ( 3999) hydrogen bonds : bond 0.04851 / 3.30 ( 138) hydrogen bonds : angle 4.90224 / 3.55 ( 411) link_ALPHA1-4 : bond 0.00272 / 0.14 ( 1) link_ALPHA1-4 : angle 1.76117 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.125 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7333 (tt0) REVERT: A 265 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6852 (mtmt) REVERT: A 300 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6727 (mp0) REVERT: A 304 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7777 (tp30) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.7581 time to fit residues: 26.3864 Evaluate side-chains 36 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110845 restraints weight = 3023.842| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.03 r_work: 0.3144 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2946 Z= 0.126 Angle : 0.494 4.719 4002 Z= 0.259 Chirality : 0.041 0.122 440 Planarity : 0.004 0.040 515 Dihedral : 4.661 51.259 427 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.36 % Allowed : 14.86 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.43), residues: 366 helix: 1.12 (0.36), residues: 180 sheet: 0.32 (1.05), residues: 24 loop : 1.13 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.014 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 2945) covalent geometry : angle 0.49223 / 0.26 ( 3999) hydrogen bonds : bond 0.04712 / 3.21 ( 138) hydrogen bonds : angle 4.85798 / 3.51 ( 411) link_ALPHA1-4 : bond 0.00261 / 0.14 ( 1) link_ALPHA1-4 : angle 1.73775 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.119 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7296 (tt0) REVERT: A 300 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6719 (mp0) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.7153 time to fit residues: 25.5690 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111143 restraints weight = 3037.692| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.03 r_work: 0.3147 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2946 Z= 0.122 Angle : 0.489 4.710 4002 Z= 0.257 Chirality : 0.041 0.121 440 Planarity : 0.004 0.039 515 Dihedral : 4.633 51.366 427 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.03 % Allowed : 15.54 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.43), residues: 366 helix: 1.15 (0.37), residues: 180 sheet: 0.48 (1.09), residues: 23 loop : 1.16 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.012 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 2945) covalent geometry : angle 0.48737 / 0.26 ( 3999) hydrogen bonds : bond 0.04602 / 3.13 ( 138) hydrogen bonds : angle 4.82696 / 3.49 ( 411) link_ALPHA1-4 : bond 0.00265 / 0.14 ( 1) link_ALPHA1-4 : angle 1.70510 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.126 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7302 (tt0) REVERT: A 300 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6725 (mp0) REVERT: A 304 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7776 (tp30) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.6861 time to fit residues: 23.2270 Evaluate side-chains 35 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 227 ASN A 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110933 restraints weight = 3077.585| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.05 r_work: 0.3143 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2946 Z= 0.123 Angle : 0.490 4.718 4002 Z= 0.258 Chirality : 0.041 0.121 440 Planarity : 0.004 0.039 515 Dihedral : 4.650 51.350 427 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.69 % Allowed : 15.88 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.43), residues: 366 helix: 1.16 (0.36), residues: 180 sheet: 0.35 (1.04), residues: 24 loop : 1.13 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.013 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 2945) covalent geometry : angle 0.48818 / 0.26 ( 3999) hydrogen bonds : bond 0.04606 / 3.13 ( 138) hydrogen bonds : angle 4.82028 / 3.49 ( 411) link_ALPHA1-4 : bond 0.00237 / 0.12 ( 1) link_ALPHA1-4 : angle 1.69994 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.120 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7318 (tt0) REVERT: A 300 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6729 (mp0) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.7367 time to fit residues: 24.1934 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111175 restraints weight = 3127.976| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.06 r_work: 0.3144 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2946 Z= 0.119 Angle : 0.486 4.702 4002 Z= 0.256 Chirality : 0.041 0.121 440 Planarity : 0.004 0.038 515 Dihedral : 4.624 51.414 427 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.03 % Allowed : 15.54 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.43), residues: 366 helix: 1.19 (0.36), residues: 180 sheet: 0.50 (1.08), residues: 23 loop : 1.18 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR A 309 PHE 0.013 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.003 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 2945) covalent geometry : angle 0.48402 / 0.26 ( 3999) hydrogen bonds : bond 0.04531 / 3.08 ( 138) hydrogen bonds : angle 4.80355 / 3.48 ( 411) link_ALPHA1-4 : bond 0.00239 / 0.13 ( 1) link_ALPHA1-4 : angle 1.68286 / 0.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.121 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7325 (tt0) REVERT: A 300 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6746 (mp0) REVERT: A 304 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7720 (tp30) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.6963 time to fit residues: 24.2627 Evaluate side-chains 36 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110686 restraints weight = 3106.134| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.05 r_work: 0.3139 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2946 Z= 0.129 Angle : 0.501 4.755 4002 Z= 0.264 Chirality : 0.041 0.123 440 Planarity : 0.004 0.038 515 Dihedral : 4.667 51.256 427 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.69 % Allowed : 15.88 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.43), residues: 366 helix: 1.15 (0.36), residues: 180 sheet: 0.35 (1.04), residues: 24 loop : 1.16 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.011 0.001 TYR A 309 PHE 0.013 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.002 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2945) covalent geometry : angle 0.49864 / 0.26 ( 3999) hydrogen bonds : bond 0.04685 / 3.18 ( 138) hydrogen bonds : angle 4.83733 / 3.50 ( 411) link_ALPHA1-4 : bond 0.00271 / 0.14 ( 1) link_ALPHA1-4 : angle 1.71993 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.125 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7326 (tt0) REVERT: A 300 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6731 (mp0) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.7289 time to fit residues: 24.6461 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.110651 restraints weight = 3067.097| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.04 r_work: 0.3139 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2946 Z= 0.128 Angle : 0.501 4.725 4002 Z= 0.264 Chirality : 0.041 0.125 440 Planarity : 0.004 0.038 515 Dihedral : 4.648 51.267 427 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.69 % Allowed : 15.54 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.43), residues: 366 helix: 1.13 (0.36), residues: 180 sheet: 0.35 (1.04), residues: 24 loop : 1.15 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.011 0.001 TYR A 309 PHE 0.013 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.002 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 2945) covalent geometry : angle 0.49866 / 0.26 ( 3999) hydrogen bonds : bond 0.04678 / 3.18 ( 138) hydrogen bonds : angle 4.84033 / 3.50 ( 411) link_ALPHA1-4 : bond 0.00241 / 0.13 ( 1) link_ALPHA1-4 : angle 1.81389 / 0.84 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.126 Fit side-chains TARDY: cannot create tardy model for: "VAL A 209 " (corrupted residue). Skipping it. REVERT: A 164 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7326 (tt0) REVERT: A 300 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6740 (mp0) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.6608 time to fit residues: 22.3637 Evaluate side-chains 34 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 279 GLN A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109871 restraints weight = 3104.740| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.05 r_work: 0.3129 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2946 Z= 0.138 Angle : 0.514 4.768 4002 Z= 0.271 Chirality : 0.042 0.129 440 Planarity : 0.004 0.038 515 Dihedral : 4.715 51.059 427 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.35 % Allowed : 16.22 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.42), residues: 366 helix: 1.08 (0.36), residues: 180 sheet: 0.34 (1.03), residues: 24 loop : 1.15 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.011 0.001 TYR A 309 PHE 0.014 0.002 PHE A 73 TRP 0.010 0.001 TRP A 184 HIS 0.002 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 2945) covalent geometry : angle 0.51169 / 0.27 ( 3999) hydrogen bonds : bond 0.04857 / 3.30 ( 138) hydrogen bonds : angle 4.88288 / 3.53 ( 411) link_ALPHA1-4 : bond 0.00304 / 0.16 ( 1) link_ALPHA1-4 : angle 1.83638 / 0.86 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.57 seconds wall clock time: 21 minutes 17.76 seconds (1277.76 seconds total)